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(-) Description

Title :  CRYSTAL STRUCTURE OF VALACYCLOVIR HYDROLASE S122A MUTANT
 
Authors :  L. Lai, Z. Xu, G. L. Amidon
Date :  20 Dec 06  (Deposition) - 05 Feb 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha/Beta Hydrolase Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Lai, Z. Xu, J. Zhou, K. D. Lee, G. L. Amidon
Molecular Basis Of Prodrug Activation By Human Valacyclovirase, An Alpha-Amino Acid Ester Hydrolase.
J. Biol. Chem. V. 283 9318 2008
PubMed-ID: 18256025  |  Reference-DOI: 10.1074/JBC.M709530200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VALACYCLOVIR HYDROLASE
    ChainsA
    EC Number3.1.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET17B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneBPHL
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymVACVASE, BIPHENYL HYDROLASE-LIKE PROTEIN, BIPHENYL HYDROLASE-RELATED PROTEIN, BPH-RP, BREAST EPITHELIAL MUCIN-ASSOCIATED ANTIGEN, MCNAA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2MN1Ligand/IonMANGANESE (II) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:35 , GLU A:57 , ASP A:78 , HIS A:84 , HOH A:476BINDING SITE FOR RESIDUE MN A 301
2AC2SOFTWAREASP A:204 , HOH A:474 , HOH A:475BINDING SITE FOR RESIDUE MG A 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OCL)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:86 -Pro A:87
2Pro A:87 -Pro A:88

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OCL)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPASE_SERPS00120 Lipases, serine active site.BPHL_HUMAN133-142  1A:116-125

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000003803791cENSE00001484766chr6:3118926-3119081156BPHL_HUMAN1-36360--
1.3aENST000003803793aENSE00001975620chr6:3123891-3123994104BPHL_HUMAN36-71361A:21-5434
1.4bENST000003803794bENSE00001985048chr6:3127476-3127642167BPHL_HUMAN71-126561A:54-10956
1.5ENST000003803795ENSE00001971814chr6:3129279-3129432154BPHL_HUMAN127-178521A:110-16152
1.6bENST000003803796bENSE00001989101chr6:3137596-3137727132BPHL_HUMAN178-222451A:161-20545
1.7cENST000003803797cENSE00001968789chr6:3140620-3140743124BPHL_HUMAN222-263421A:205-24642
1.9iENST000003803799iENSE00001923833chr6:3152722-31538121091BPHL_HUMAN263-291291A:246-27429

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:254
 aligned with BPHL_HUMAN | Q86WA6 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:254
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287    
           BPHL_HUMAN    38 SVTSAKVAVNGVQLHYQQTGEGDHAVLLLPGMLGSGETDFGPQLKNLNKKLFTVVAWDPRGYGHSRPPDRDFPADFFERDAKDAVDLMKALKFKKVSLLGWSDGGITALIAAAKYPSYIHKMVIWGANAYVTDEDSMIYEGIRDVSKWSERTRKPLEALYGYDYFARTCEKWVDGIRQFKHLPDGNICRHLLPRVQCPALIVHGEKDPLVPRFHADFIHKHVKGSRLHLMPEGKHNLHLRFADEFNKLAEDFLQ 291
               SCOP domains d2ocla_ A: automated matches                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..eeeeeeeee...eeeeee.....hhhhhhhhhhhhh....eeeeee.................hhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh...eeeeee......hhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------LIPASE_SER----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a  PDB: A:21-54           -------------------------------------------------------Exon 1.5  PDB: A:110-161 UniProt: 127-178           -------------------------------------------Exon 1.7c  PDB: A:205-246 UniProt: 222-263---------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------Exon 1.4b  PDB: A:54-109 UniProt: 71-126                ---------------------------------------------------Exon 1.6b  PDB: A:161-205 UniProt: 178-222   ----------------------------------------Exon 1.9i  PDB: A:246-274     Transcript 1 (2)
                 2ocl A  21 SVTSAKVAVNGVQLHYQQTGEGDHAVLLLPGMLGSGETDFGPQLKNLNKKLFTVVAWDPRGYGHSRPPDRDFPADFFERDAKDAVDLMKALKFKKVSLLGWADGGITALIAAAKYPSYIHKMVIWGANAYVTDEDSMIYEGIRDVSKWSERTRKPLEALYGYDYFARTCEKWVDGIRQFKHLPDGNICRHLLPRVQCPALIVHGEKDPLVPRFHADFIHKHVKGSRLHLMPEGKHNLHLRFADEFNKLAEDFLQ 274
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270    

   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2OCL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2OCL)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BPHL_HUMAN | Q86WA6)
molecular function
    GO:0047658    alpha-amino-acid esterase activity    Catalysis of the reaction: an alpha-amino acid ester + H2O = an alpha-amino acid + an alcohol.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
biological process
    GO:0006520    cellular amino acid metabolic process    The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
    GO:0009636    response to toxic substance    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.
    GO:0006805    xenobiotic metabolic process    The chemical reactions and pathways involving a xenobiotic compound, a compound foreign to living organisms. Used of chemical compounds, e.g. a xenobiotic chemical, such as a pesticide.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005741    mitochondrial outer membrane    The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        BPHL_HUMAN | Q86WA62ocg 2oci 2ock

(-) Related Entries Specified in the PDB File

2ocg CRYSTAL STRUCTURE OF HUMAN VALACYCLOVIR HYDROLASE
2oci CRYSTAL STRUCTURE OF VALACYCLOVIR HYDROLASE COMPLEXED WITH A PRODUCT ANALOGUE
2ock CRYSTAL STRUCTURE OF VALACYCLOVIR HYDROLASE D123N MUTANT